Carbohydrates

 

sugars2
Carbohydrates (saccharides), the most abundant product of photosynthesis, play an important role in the energetic metabolism of living species and the signaling and immunological responses and are a fundamental component of the external cell wall of many organisms. In addition, saccharides are present in a variety of emerging classes of biomimetic materials. Furthermore, due to their cryo- and anhydro-protective properties, many sugars have been shown to be effective stabilizers of biological components, such as proteins and membranes, in the low-temperature or dehydrated states. This class of compounds encompasses a huge variety of possible monomeric units (differing in stereochemistry and functionalization) that can be connected in chains presenting a virtually infinite number of possible residue sequences, linkage types, and degrees of branching.

The large size of most oligosaccharides warrants the use of a coarse-grained model, yet the complexity of carbohydrate physico-chemical properties makes this a very challenging undertaking. Recently, Martini has been parameterized for common mono- and disaccharides [1] that can serve as a basis for further carbohydrate modeling. Based on this model, oligosaccharides such as amylose [1], and cellulose [2] have been parameterized as well. Most recent addition is the important class of glyco-lipids [3], with parameters for MGDG, DGDG, SQDG, PI, PIPn, GCER, and GM1. The abililty of GM1 to recruit membrane proteins has also been studied [4].

  • [1] C.A. Lopez, A. Rzepiela, A.H. de Vries, L. Dijkhuizen, P.H. Huenenberger, S.J. Marrink. The Martini coarse grained force field: extension to carbohydrates. J. Chem. Th. Comp., 5:3195-3210, 2009.
  • [2] J. Wohlert, L.A. Berglund. A coarse-grained model for molecular dynamics simulations of native cellulose. J. Chem. Theo. Comp. 7:753-760, 2011.
  • [3] C.A. Lopez, Z. Sovova, F.J. van Eerden, A.H. de Vries, S.J. Marrink. Martini force field parameters for glycolipids. J. Chem. Theory Comput., in press, 2013. DOI:10.1021/ct3009655. abstract
  • [4] D.H. de Jong, C.A. Lopez, S.J. Marrink.Molecular view on protein sorting into liquid-ordered membrane domains mediated by gangliosides and lipid anchors. Farad. Discuss., accepted. DOI:10.1039/C2FD20086D. abstract